Primaschema

🚨 Migration to v1 scheme specification in progress

A toolkit for fetching, validating and interrogating tiled amplicon PCR primer scheme definitions. Provides convenient programmatic accesss to the PHA4GE primer-schemes repository, a community repository of tiled amplicons primer schemes.

Install (Python 3.8+)

# Latest stable release
pip install primaschema

# From main branch
git clone https://github.com/pha4ge/primaschema
pip install ./primaschema

# Development
git clone https://github.com/pha4ge/primaschema.git
cd primaschema
pip install --editable '.[dev]'
pre-commit install
pytest

Some Primaschema commands use components from the primer-schemes repository. To show Primaschema where to find these, create the environment variable PRIMER_SCHEMES_PATH pointing to the location of the primer-schemes directory on your machine:

git clone https://github.com/pha4ge/primer-schemes.git
export PRIMER_SCHEMES_PATH="/path/to/primer-schemes"

Usage

% primaschema -h
usage: primaschema [-h] [--version]
                   {validate,build,build-manifest,hash-ref,hash-bed,diff,6to7,7to6,plot,show-intervals,show-discordant-primers,subset,sync} ...

positional arguments:
  {validate,build,build-manifest,hash-ref,hash-bed,diff,6to7,7to6,plot,show-intervals,show-discordant-primers,subset,sync}
    validate            Validate one or more primer scheme definitions comprising info.yml, primer.bed and reference.fasta
    build               Build one or more primer scheme definitions comprising info.yml, primer.bed and reference.fasta
    build-manifest      Build a complete manifest of schemes contained in the specified directory
    hash-ref            Generate reference sequence checksum
    hash-bed            Generate a bed file checksum
    diff                Show the symmetric difference of records in two bed files
    6to7                Convert a 6 column scheme.bed file to a 7 column primer.bed file using reference backfill
    7to6                Convert a 7 column primer.bed file to a 6 column scheme.bed file by removing a column
    plot                Plot amplicon and primer coords from 7 column primer.bed
    show-intervals      Show amplicon start and end coordinates given a BED file of primer coordinates
    show-discordant-primers
                        Show primer records with sequences not matching the reference sequence
    subset              Extract a primer.bed and reference.fasta scheme subset for a single chromosome
    sync                Retrieve/update local copy of remote primer scheme repository

options:
  -h, --help            show this help message and exit
  --version             show program's version number and exit